PXD041358

PXD041358 is an original dataset announced via ProteomeXchange.

Title	GeLC-FAIMS-MS Workflow for In-Depth Middle-Down Proteomics
Description	Middle-down proteomics is an analytical approach whereby protein samples are digested with proteases such as Glu-C to generate large peptides (>3 kDa) that are then analyzed by mass spectrometry. This method is useful for characterizing high-molecular-weight proteins that are difficult to detect by top-down proteomics, in which intact proteins are analyzed by mass spectrometry. In this study, we applied GeLC-FAIMS-MS, a multidimensional separation workflow that combines gel-based prefractionation with LC-FAIMS Orbitrap mass spectrometry, for deep middle-down proteomics. Middle-down peptides obtained under the condition of optimized limited Glu-C digestion were first size-fractionated by polyacrylamide gel electrophoresis, followed by C4 reversed-phase liquid chromatography separation and additional ion mobility fractionation, resulting in a significant increase in peptide length detectable by mass spectrometry. In addition to global analysis, the GeLC-FAIMS concept can also be applied to targeted middle-down proteomics, where only proteins in the desired molecular weight range are gel-fractionated and their Glu-C digestion products are analyzed, as demonstrated by targeted analysis of integrins in exosomes. In-depth middle-down proteomics achieved by global and targeted GeLC-FAIMS-MS allows the exploration of proteoform information not covered by conventional top-down proteomics via increase in the number of detectable proteoforms and improvement in sequence coverage.
HostingRepository	PRIDE
AnnounceDate	2024-11-20
AnnouncementXML	Submission_2024-11-20_07:01:25.164.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Andreas Tholey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-05 13:25:35	ID requested
⏵ 1	2024-11-20 07:01:25	announced

10.1002/PMIC.202200431;

submitter keyword: Glu-C Digestion,Proteoform, Middle-down Proteomics, LC-FAIMS Orbitrap Mass Spectrometry, PEPPI-MS, AnExSP

Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
contact email	a.tholey@iem.uni-kiel.de
lab head
Andreas Tholey
contact affiliation	Systematic Proteome Research & Bioanalytics, University of Kiel
contact email	a.tholey@iem.uni-kiel.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/11/PXD041358

PRIDE project URI

• PRIDE
  1. PXD041358
     1. Label: PRIDE project
     2. Name: GeLC-FAIMS-MS Workflow for In-Depth Middle-Down Proteomics